ETV3L

Summary

ETV3L (ETS variant transcription factor 3 like, HGNC:33834) is a protein-coding gene on chromosome 1q23.1, encoding ETS translocation variant 3-like protein (Q6ZN32). Transcriptional regulator.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in cell differentiation and regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 440695 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 86 total
• MANE Select transcript: NM_001004341

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33834
Approved symbol	ETV3L
Name	ETS variant transcription factor 3 like
Location	1q23.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ16478
Ensembl gene	ENSG00000253831
Ensembl biotype	protein_coding
OMIM	621105
Entrez	440695

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000454449, ENST00000671886, ENST00000671942, ENST00000672100, ENST00000884020, ENST00000933010, ENST00000933011, ENST00000933012

RefSeq mRNA: 1 — MANE Select: NM_001004341 NM_001004341

CCDS: CCDS30893

Canonical transcript exons

ENST00000454449 — 5 exons

Exon	Start	End
ENSE00002213511	157098706	157098895
ENSE00002243813	157099141	157099378
ENSE00002294199	157092043	157093127
ENSE00002300649	157097868	157097988
ENSE00002300735	157099466	157099808

Expression profiles

Bgee: expression breadth broad, 32 present calls, max score 84.17.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 4.5290 / max 4447.5156, expressed in 74 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15249	4.0356	21
15247	0.2573	41
15250	0.1645	4
15248	0.0549	3
15252	0.0166	10

Top tissues by expression

129 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
thymus	UBERON:0002370	84.17	silver quality
quadriceps femoris	UBERON:0001377	77.53	gold quality
cerebellar vermis	UBERON:0004720	76.66	gold quality
nucleus accumbens	UBERON:0001882	52.60	gold quality
vermiform appendix	UBERON:0001154	50.93	gold quality
monocyte	CL:0000576	47.99	silver quality
leukocyte	CL:0000738	47.00	silver quality
primary visual cortex	UBERON:0002436	46.18	silver quality
granulocyte	CL:0000094	44.79	silver quality
prefrontal cortex	UBERON:0000451	43.22	gold quality
Brodmann (1909) area 9	UBERON:0013540	41.58	silver quality
putamen	UBERON:0001874	41.38	gold quality
colonic epithelium	UBERON:0000397	41.24	gold quality
frontal cortex	UBERON:0001870	41.00	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	39.99	silver quality
thoracic mammary gland	UBERON:0005200	39.65	gold quality
caudate nucleus	UBERON:0001873	39.43	gold quality
cerebral cortex	UBERON:0000956	38.59	gold quality
right frontal lobe	UBERON:0002810	38.50	silver quality
amygdala	UBERON:0001876	38.03	silver quality
temporal lobe	UBERON:0001871	37.93	silver quality
tonsil	UBERON:0002372	37.21	silver quality
right uterine tube	UBERON:0001302	36.50	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
sural nerve	UBERON:0015488	36.27	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
brain	UBERON:0000955	35.69	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.61	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting ETV3L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-8085	99.28	67.56	2362
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-5587-5P	99.07	68.58	838
HSA-MIR-6756-3P	98.94	66.79	1104
HSA-MIR-7113-3P	98.75	65.71	1120
HSA-MIR-5011-3P	98.63	64.81	638
HSA-MIR-4703-5P	98.53	70.13	1645
HSA-MIR-4766-3P	98.48	67.94	1347
HSA-MIR-6742-3P	97.95	64.50	1490
HSA-MIR-299-3P	97.73	66.67	773
HSA-MIR-296-5P	97.61	64.02	851
HSA-MIR-4286	97.20	64.37	1587
HSA-MIR-3116	97.07	65.78	1324
HSA-MIR-339-5P	96.73	66.01	820
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-4761-3P	96.27	66.26	524

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Etv3l	ENSMUSG00000118505
rattus_norvegicus	Etv3l	ENSRNOG00000043511

Paralogs (28): ETV1 (ENSG00000006468), ETV7 (ENSG00000010030), SPI1 (ENSG00000066336), ELF4 (ENSG00000102034), ETV2 (ENSG00000105672), ERF (ENSG00000105722), ELF2 (ENSG00000109381), ELK3 (ENSG00000111145), ETV3 (ENSG00000117036), ELF1 (ENSG00000120690), SPDEF (ENSG00000124664), ELK1 (ENSG00000126767), ETS1 (ENSG00000134954), EHF (ENSG00000135373), ELF5 (ENSG00000135374), ETV6 (ENSG00000139083), FLI1 (ENSG00000151702), GABPA (ENSG00000154727), ERG (ENSG00000157554), ETS2 (ENSG00000157557), ELK4 (ENSG00000158711), ELF3 (ENSG00000163435), FEV (ENSG00000163497), SPIC (ENSG00000166211), ETV4 (ENSG00000175832), ETV5 (ENSG00000244405), ERFL (ENSG00000268041), SPIB (ENSG00000269404)

Protein

Protein identifiers

ETS translocation variant 3-like protein — Q6ZN32 (reviewed: Q6ZN32)

All UniProt accessions (1): Q6ZN32

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional regulator.

Subcellular location. Nucleus.

Similarity. Belongs to the ETS family.

RefSeq proteins (1): NP_001004341* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000418	Ets_dom	Domain
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily
IPR046328	ETS_fam	Family

Pfam: PF00178

UniProt features (7 total): sequence variant 4, chain 1, DNA-binding region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZN32-F1	56.93	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR4306, MIR6721_5P, MIR4644, MIR185_5P, MIR8085, MIR6731_5P, MIR6852_5P, MIR4766_3P, GSE11884_WT_VS_FURIN_KO_NAIVE_CD4_TCELL_DN, HE_LIM_SUN_FETAL_LUNG_C2_ADC_1_CELL, HE_LIM_SUN_FETAL_LUNG_C2_ADC_2_CELL, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), cell differentiation (GO:0030154), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	1
cellular developmental process	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
DNA binding	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

240 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ETV3L	LRRC71	Q8N4P6	596
ETV3L	C17orf107	Q6ZR85	447
ETV3L	WDR86	Q86TI4	444
ETV3L	LRRIQ4	A6NIV6	418
ETV3L	PEAR1	Q5VY43	405
ETV3L	UBXN10	Q96LJ8	402
ETV3L	SSX7	Q7RTT5	400
ETV3L	NCAPD3	P42695	399
ETV3L	ZNHIT1	O43257	355
ETV3L	PRR13	Q9NZ81	352
ETV3L	LRRC38	Q5VT99	349
ETV3L	VAT1L	Q9HCJ6	339
ETV3L	CRACD	Q6ZU35	333
ETV3L	UBE2QL1	A1L167	328
ETV3L	INSRR	P14616	327

IntAct

4 interactions, top by confidence:

A	B	Type	Score
NOTO	ETV3L	psi-mi:“MI:0915”(physical association)	0.560
ETV3L	NOTO	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (1): ETV3L (Two-hybrid)

ESM2 similar proteins: A0A5F9ZHS7, A1YGK1, A2T7E6, A8MZG2, O08574, O43593, O60393, O75593, O88621, O95231, P0C1T1, P0CG20, P20428, P97609, Q04667, Q17QR5, Q2KIS6, Q2M1V0, Q2T9Q7, Q32LE6, Q497V6, Q5JUK2, Q5M844, Q5RJB0, Q5TGS1, Q61645, Q61657, Q6ZMY3, Q6ZN32, Q6ZNG2, Q7RTU1, Q8BZW2, Q8CGW9, Q8IWN7, Q8IXT2, Q8IZ20, Q8N1L9, Q8N7G0, Q8N944, Q8N9Y4

Diamond homologs: A0A1W2PQ73, A0JN51, A1A4L6, A1YF15, A1YG61, A1YG91, A2D4Z7, A2T737, A2T762, A3FEM2, A4GTP4, A8WFJ9, O00321, O01519, O70132, O70273, O95238, P01105, P10157, P11308, P11536, P13474, P14921, P15036, P15037, P15062, P18755, P18756, P19102, P19419, P20105, P26323, P27577, P28322, P28324, P29773, P29774, P29775, P29776, P32519

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

86 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	15
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

822 predictions. Top by Δscore:

Variant	Effect	Δscore
1:157097866:A:AC	donor_gain	1.0000
1:157097867:C:CC	donor_gain	1.0000
1:157099135:TCTCA:T	donor_loss	1.0000
1:157099136:CTCA:C	donor_loss	1.0000
1:157099137:TCA:T	donor_loss	1.0000
1:157099138:CACCT:C	donor_loss	1.0000
1:157099139:AC:A	donor_loss	1.0000
1:157099140:C:CA	donor_loss	1.0000
1:157099157:G:C	donor_gain	1.0000
1:157097989:C:CC	acceptor_gain	0.9900
1:157098794:T:TA	donor_gain	0.9900
1:157098795:C:A	donor_gain	0.9900
1:157099187:T:TA	donor_gain	0.9900
1:157099208:C:CT	donor_gain	0.9900
1:157099248:T:A	donor_gain	0.9900
1:157099460:GCTCA:G	donor_loss	0.9900
1:157099461:CTCA:C	donor_loss	0.9900
1:157099462:TCA:T	donor_loss	0.9900
1:157099463:CA:C	donor_loss	0.9900
1:157099464:ACCTG:A	donor_loss	0.9900
1:157099465:C:A	donor_loss	0.9900
1:157097859:AGCAC:A	donor_loss	0.9800
1:157097860:GCAC:G	donor_loss	0.9800
1:157097861:CACT:C	donor_loss	0.9800
1:157097862:AC:A	donor_loss	0.9800
1:157097863:CT:C	donor_loss	0.9800
1:157097864:TCACG:T	donor_loss	0.9800
1:157097865:C:CC	donor_loss	0.9800
1:157097866:ACGG:A	donor_loss	0.9800
1:157097867:CG:C	donor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000074639 (1:157097259 G>A,C,T), RS1000108424 (1:157097686 G>A), RS1000461633 (1:157091983 C>T), RS1000757230 (1:157093968 T>C), RS1000923900 (1:157101103 A>C), RS1001108835 (1:157098590 G>A), RS1001115537 (1:157096268 C>A,T), RS1001654696 (1:157097675 G>A), RS1001860483 (1:157092911 C>T), RS1002203764 (1:157096670 C>T), RS1002460360 (1:157091649 G>A), RS1002523115 (1:157099861 C>A), RS1002796414 (1:157096240 C>G,T), RS1002911145 (1:157096516 G>T), RS1002921950 (1:157098981 G>A,T)

Disease associations

OMIM: gene MIM:621105 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST000253_11	Attention deficit hyperactivity disorder and conduct disorder	8.000000e-06
GCST009597_33	Multiple sclerosis	2.000000e-06
GCST010002_368	Refractive error	7.000000e-38
GCST010697_36	Cortical surface area (min-P)	5.000000e-08
GCST010698_82	Subcortical volume (min-P)	4.000000e-20
GCST010699_62	Brain morphology (min-P)	2.000000e-26
GCST010700_48	Cortical thickness (MOSTest)	2.000000e-10
GCST010701_53	Cortical surface area (MOSTest)	1.000000e-16
GCST010702_160	Subcortical volume (MOSTest)	1.000000e-21
GCST010703_149	Brain morphology (MOSTest)	2.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
Benzo(a)pyrene	affects methylation	1
Diethylhexyl Phthalate	decreases expression	1
Lipopolysaccharides	affects cotreatment, increases expression, affects response to substance	1
Urethane	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.